If you're using a BES, you should have a direct connection to your corporate network through it, so you shouldn't need a VPN (which I've never heard of anyway!).
The BlackBerry Browser routes through the BES, not your carrier's network (as the WAP browser does), or the Internet (as the Internet Browser does).
I know this because if I use the WAP browser to go to
Yahoo!, I come up with Cingular's MediaNet version of that site rather than Yahoo's which I get with both the Internet Browser and the BlackBerry Browser.
If I use the BlackBerry Browser to try to get to a site blocked by my company, I get their Site Blocked page, but can get to it with the Internet and WAP Browsers.
You will have problems, however, if you need to authenticate into your company's Intranet sites. I don't know if there are any solutions to that problem. However, if you're trying to use something like a remote control program, it should work as long as you can set it to use your BES connection.